This is a SQLyog question, not a MONyog question. Please post in the correct category. I am moving you!
I can confirm that there is some issue. Also when connecting to a table with 10.000 rows and a LIMIT setting of 100, 6.1 is much slower than 6.07. What seems to indicate that the full table is loaded!
Maybe you noticed that the 'preferences' dialogue was rearranged. I think it could be a bug related to that, even though HISTORY tells that LIMIT is used. The statement from HISTORY executed from the editor in 6.1 seems to be as fast as is the 6.07 GUI.
It is Indian holiday today and we will only be able to get closer tomorrow.